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| - | [[Image:1qgh.gif|left|200px]]<br /><applet load="1qgh" size="350" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1qgh, resolution 2.35Å" /> | |
| - | '''THE X-RAY STRUCTURE OF THE UNUSUAL DODECAMERIC FERRITIN FROM LISTERIA INNOCUA, REVEALS A NOVEL INTERSUBUNIT IRON BINDING SITE.'''<br /> | |
| | | | |
| - | ==Overview== | + | ==THE X-RAY STRUCTURE OF THE UNUSUAL DODECAMERIC FERRITIN FROM LISTERIA INNOCUA, REVEALS A NOVEL INTERSUBUNIT IRON BINDING SITE.== |
| - | Ferritin is characterized by a highly conserved architecture that, comprises 24 subunits assembled into a spherical cage with 432 symmetry., The only known exception is the dodecameric ferritin from Listeria, innocua. The structure of Listeria ferritin has been determined to a, resolution of 2.35 A by molecular replacement, using as a search model the, structure of Dps from Escherichia coli. The Listeria 12-mer is endowed, with 23 symmetry and displays the functionally relevant structural, features of the ferritin 24-mer, namely the negatively charged channels, along the three-fold symmetry axes that serve for iron entry into the, cavity and a negatively charged internal cavity for iron deposition. The, electron density map shows 12 iron ions on the inner surface of the hollow, core, at the interface between monomers related by two-fold axes. Analysis, of the nature and stereochemistry of the iron-binding ligands reveals, strong similarities with known ferroxidase sites. The L. innocua ferritin, site, however, is the first described so far that has ligands belonging to, two different subunits and is not contained within a four-helix bundle. | + | <StructureSection load='1qgh' size='340' side='right'caption='[[1qgh]], [[Resolution|resolution]] 2.35Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1qgh]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Listeria_innocua Listeria innocua]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QGH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QGH FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qgh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qgh OCA], [https://pdbe.org/1qgh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qgh RCSB], [https://www.ebi.ac.uk/pdbsum/1qgh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qgh ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DPS_LISIN DPS_LISIN] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Does not bind DNA.<ref>PMID:12383509</ref> <ref>PMID:15823015</ref> <ref>PMID:9013563</ref> |
| | + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qg/1qgh_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qgh ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Ferritin is characterized by a highly conserved architecture that comprises 24 subunits assembled into a spherical cage with 432 symmetry. The only known exception is the dodecameric ferritin from Listeria innocua. The structure of Listeria ferritin has been determined to a resolution of 2.35 A by molecular replacement, using as a search model the structure of Dps from Escherichia coli. The Listeria 12-mer is endowed with 23 symmetry and displays the functionally relevant structural features of the ferritin 24-mer, namely the negatively charged channels along the three-fold symmetry axes that serve for iron entry into the cavity and a negatively charged internal cavity for iron deposition. The electron density map shows 12 iron ions on the inner surface of the hollow core, at the interface between monomers related by two-fold axes. Analysis of the nature and stereochemistry of the iron-binding ligands reveals strong similarities with known ferroxidase sites. The L. innocua ferritin site, however, is the first described so far that has ligands belonging to two different subunits and is not contained within a four-helix bundle. |
| | | | |
| - | ==About this Structure==
| + | The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site.,Ilari A, Stefanini S, Chiancone E, Tsernoglou D Nat Struct Biol. 2000 Jan;7(1):38-43. PMID:10625425<ref>PMID:10625425</ref> |
| - | 1QGH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Listeria_innocua Listeria innocua] with <scene name='pdbligand=FE:'>FE</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Sites: <scene name='pdbsite=ASA:Fe-Binding+Site'>ASA</scene>, <scene name='pdbsite=ASB:Fe-Binding+Site'>ASB</scene>, <scene name='pdbsite=ASC:Fe-Binding+Site'>ASC</scene>, <scene name='pdbsite=ASD:Fe-Binding+Site'>ASD</scene>, <scene name='pdbsite=ASE:Fe-Binding+Site'>ASE</scene>, <scene name='pdbsite=ASF:Fe-Binding+Site'>ASF</scene>, <scene name='pdbsite=ASG:Fe-Binding+Site'>ASG</scene>, <scene name='pdbsite=ASH:Fe-Binding+Site'>ASH</scene>, <scene name='pdbsite=ASI:Fe-Binding+Site'>ASI</scene>, <scene name='pdbsite=ASJ:Fe-Binding+Site'>ASJ</scene>, <scene name='pdbsite=ASK:Fe-Binding+Site'>ASK</scene> and <scene name='pdbsite=ASL:Fe-Binding+Site'>ASL</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QGH OCA].
| + | |
| | | | |
| - | ==Reference==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site., Ilari A, Stefanini S, Chiancone E, Tsernoglou D, Nat Struct Biol. 2000 Jan;7(1):38-43. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10625425 10625425]
| + | </div> |
| - | [[Category: Listeria innocua]]
| + | <div class="pdbe-citations 1qgh" style="background-color:#fffaf0;"></div> |
| - | [[Category: Single protein]]
| + | |
| - | [[Category: Chiancone, E.]]
| + | |
| - | [[Category: Ilari, A.]]
| + | |
| - | [[Category: Stefanini, S.]]
| + | |
| - | [[Category: Tsernoglou, D.]]
| + | |
| - | [[Category: FE]]
| + | |
| - | [[Category: ferritin]]
| + | |
| | | | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:00:08 2008''
| + | ==See Also== |
| | + | *[[Ferritin 3D structures|Ferritin 3D structures]] |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | + | [[Category: Listeria innocua]] |
| | + | [[Category: Chiancone E]] |
| | + | [[Category: Ilari A]] |
| | + | [[Category: Stefanini S]] |
| | + | [[Category: Tsernoglou D]] |
| Structural highlights
Function
DPS_LISIN Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Does not bind DNA.[1] [2] [3]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Ferritin is characterized by a highly conserved architecture that comprises 24 subunits assembled into a spherical cage with 432 symmetry. The only known exception is the dodecameric ferritin from Listeria innocua. The structure of Listeria ferritin has been determined to a resolution of 2.35 A by molecular replacement, using as a search model the structure of Dps from Escherichia coli. The Listeria 12-mer is endowed with 23 symmetry and displays the functionally relevant structural features of the ferritin 24-mer, namely the negatively charged channels along the three-fold symmetry axes that serve for iron entry into the cavity and a negatively charged internal cavity for iron deposition. The electron density map shows 12 iron ions on the inner surface of the hollow core, at the interface between monomers related by two-fold axes. Analysis of the nature and stereochemistry of the iron-binding ligands reveals strong similarities with known ferroxidase sites. The L. innocua ferritin site, however, is the first described so far that has ligands belonging to two different subunits and is not contained within a four-helix bundle.
The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site.,Ilari A, Stefanini S, Chiancone E, Tsernoglou D Nat Struct Biol. 2000 Jan;7(1):38-43. PMID:10625425[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Polidoro M, De Biase D, Montagnini B, Guarrera L, Cavallo S, Valenti P, Stefanini S, Chiancone E. The expression of the dodecameric ferritin in Listeria spp. is induced by iron limitation and stationary growth phase. Gene. 2002 Aug 21;296(1-2):121-8. PMID:12383509
- ↑ Su M, Cavallo S, Stefanini S, Chiancone E, Chasteen ND. The so-called Listeria innocua ferritin is a Dps protein. Iron incorporation, detoxification, and DNA protection properties. Biochemistry. 2005 Apr 19;44(15):5572-8. PMID:15823015 doi:http://dx.doi.org/10.1021/bi0472705
- ↑ Bozzi M, Mignogna G, Stefanini S, Barra D, Longhi C, Valenti P, Chiancone E. A novel non-heme iron-binding ferritin related to the DNA-binding proteins of the Dps family in Listeria innocua. J Biol Chem. 1997 Feb 7;272(6):3259-65. PMID:9013563
- ↑ Ilari A, Stefanini S, Chiancone E, Tsernoglou D. The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site. Nat Struct Biol. 2000 Jan;7(1):38-43. PMID:10625425 doi:10.1038/71236
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